Loading Library

library(knitr)
packageVersion("knitr")
## [1] '1.20'
library(energy)
packageVersion("energy")
## [1] '1.7.5'
library(broom)
packageVersion("broom")
## [1] '0.5.0'
library(plyr)
packageVersion("plyr")
## [1] '1.8.4'
library(kableExtra)
packageVersion("kableExtra")
## [1] '0.9.0'
library(foreach)
packageVersion("foreach")
## [1] '1.4.4'
library(doParallel)
## Loading required package: iterators
## Loading required package: parallel
packageVersion("doParallel")
## [1] '1.0.14'
set.seed(0)

Simulating MPEA Surrogate over the array.

load(file = "lung_mich_curated.Rdata")
epsilon=1e-6
nominal_dcor_pvalues <- sapply(1:pathway_number, function(x) (epsilon+(sum(surrogate_dcor[[x]]>dcor_results[x])))/(1+num_simulation))
names(nominal_dcor_pvalues) <- names( pathway_collapsed)
head(sort(nominal_dcor_pvalues),10)
##           SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1 
##                                    0.0000000001 
##                MEISSNER_BRAIN_HCP_WITH_H3K27ME3 
##                                    0.0002000001 
##                               KIM_TIAL1_TARGETS 
##                                    0.0002000001 
##              MUELLER_METHYLATED_IN_GLIOBLASTOMA 
##                                    0.0004000001 
##           MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED 
##                                    0.0008000001 
##                              GU_PDEF_TARGETS_DN 
##                                    0.0009000001 
##   CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP 
##                                    0.0015000001 
## WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN 
##                                    0.0017000001 
##                HUPER_BREAST_BASAL_VS_LUMINAL_DN 
##                                    0.0025000001 
##            CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN 
##                                    0.0026000001
dcor_significant_pathways_p.value <- sort(nominal_dcor_pvalues[nominal_dcor_pvalues <0.05])
length(dcor_significant_pathways_p.value)
## [1] 118
nominal_dcor_q_values <- p.adjust(nominal_dcor_pvalues , method = "fdr")
# nominal_dcor_q_values
nominal_dcor_q_values_under_25 <- sort(nominal_dcor_q_values[nominal_dcor_q_values<0.25])
length((nominal_dcor_q_values_under_25))
## [1] 3
nominal_dcor_q_values_under_25
## SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1 
##                          0.0000002955 
##      MEISSNER_BRAIN_HCP_WITH_H3K27ME3 
##                          0.1970000985 
##                     KIM_TIAL1_TARGETS 
##                          0.1970000985

GSEA signifcanct pathways p-value and Q-value

nrow(gsea_results_significant)
## [1] 296
length(rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
## [1] 33

Identifying the pathways deemed significant in both GSEA and MPEA

Mutually_identified_in_GSEA_dcor <- intersect(names(dcor_significant_pathways_p.value), rownames(gsea_results_significant))

Mutually_identified_in_GSEA_dcor
##  [1] "GU_PDEF_TARGETS_DN"                                
##  [2] "HUPER_BREAST_BASAL_VS_LUMINAL_DN"                  
##  [3] "SABATES_COLORECTAL_ADENOMA_UP"                     
##  [4] "ENK_UV_RESPONSE_EPIDERMIS_UP"                      
##  [5] "GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN"
##  [6] "WOOD_EBV_EBNA1_TARGETS_DN"                         
##  [7] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN"    
##  [8] "WU_CELL_MIGRATION"                                 
##  [9] "JAEGER_METASTASIS_DN"                              
## [10] "AMIT_SERUM_RESPONSE_480_MCF10A"                    
## [11] "HAHTOLA_CTCL_CUTANEOUS"                            
## [12] "BAE_BRCA1_TARGETS_UP"                              
## [13] "VANTVEER_BREAST_CANCER_ESR1_DN"                    
## [14] "ONDER_CDH1_TARGETS_2_DN"                           
## [15] "LI_LUNG_CANCER"                                    
## [16] "FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL"          
## [17] "COLDREN_GEFITINIB_RESISTANCE_DN"                   
## [18] "MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP"            
## [19] "LEE_LIVER_CANCER_ACOX1_UP"                         
## [20] "JIANG_AGING_HYPOTHALAMUS_DN"                       
## [21] "CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP"     
## [22] "GAJATE_RESPONSE_TO_TRABECTEDIN_UP"                 
## [23] "KIM_HYPOXIA"                                       
## [24] "SESTO_RESPONSE_TO_UV_C1"                           
## [25] "BIOCARTA_CERAMIDE_PATHWAY"                         
## [26] "HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP"       
## [27] "MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP"        
## [28] "KEGG_GLYCOLYSIS_GLUCONEOGENESIS"                   
## [29] "HAN_SATB1_TARGETS_UP"
Mutually_identified_in_GSEA_dcor_fdr <- intersect(names(nominal_dcor_q_values_under_25),rownames(gsea_results_significant[gsea_results_significant$FDR.q.val<0.25,]))
length(Mutually_identified_in_GSEA_dcor_fdr)
## [1] 0

Identifying the pathways significant in MPEA not in GSEA

Significant_in_dcor_not_in_GSEA <- setdiff(names(dcor_significant_pathways_p.value),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(dcor_significant_pathways_p.value[Significant_in_dcor_not_in_GSEA],gsea_results[Significant_in_dcor_not_in_GSEA,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities%>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1 MEISSNER_BRAIN_HCP_WITH_H3K27ME3 KIM_TIAL1_TARGETS MUELLER_METHYLATED_IN_GLIOBLASTOMA MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP NABA_SECRETED_FACTORS DORSAM_HOXA9_TARGETS_DN DURAND_STROMA_NS_UP ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP DORN_ADENOVIRUS_INFECTION_12HR_UP WANG_BARRETTS_ESOPHAGUS_UP MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP APPIERTO_RESPONSE_TO_FENRETINIDE_DN PARK_APL_PATHOGENESIS_DN SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN SIMBULAN_UV_RESPONSE_NORMAL_DN HUPER_BREAST_BASAL_VS_LUMINAL_UP KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP BENPORATH_PROLIFERATION STEIN_ESRRA_TARGETS TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN HENDRICKS_SMARCA4_TARGETS_UP SANA_TNF_SIGNALING_DN LEE_TARGETS_OF_PTCH1_AND_SUFU_DN NABA_MATRISOME_ASSOCIATED KEGG_PROPANOATE_METABOLISM KAMIKUBO_MYELOID_CEBPA_NETWORK VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED BOYLAN_MULTIPLE_MYELOMA_D_DN REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE KEGG_CYSTEINE_AND_METHIONINE_METABOLISM KEGG_PYRUVATE_METABOLISM NAKAJIMA_EOSINOPHIL ZHAN_MULTIPLE_MYELOMA_DN HAHTOLA_SEZARY_SYNDROM_UP KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP ROSS_AML_WITH_PML_RARA_FUSION YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9 TSUNODA_CISPLATIN_RESISTANCE_DN HELLER_SILENCED_BY_METHYLATION_UP VANTVEER_BREAST_CANCER_METASTASIS_UP HAN_JNK_SINGALING_UP REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP STEARMAN_TUMOR_FIELD_EFFECT_UP STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN SU_PLACENTA ANDERSEN_LIVER_CANCER_KRT19_UP CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP LINDVALL_IMMORTALIZED_BY_TERT_UP BROWNE_HCMV_INFECTION_2HR_UP BOYLAN_MULTIPLE_MYELOMA_PCA1_UP MCDOWELL_ACUTE_LUNG_INJURY_UP DELPUECH_FOXO3_TARGETS_UP DOANE_RESPONSE_TO_ANDROGEN_UP ABE_VEGFA_TARGETS_2HR SANSOM_APC_TARGETS_UP BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN JIANG_AGING_CEREBRAL_CORTEX_DN YAMAZAKI_TCEB3_TARGETS_DN PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP ABE_VEGFA_TARGETS_30MIN ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP DORN_ADENOVIRUS_INFECTION_48HR_DN MOREIRA_RESPONSE_TO_TSA_UP MALONEY_RESPONSE_TO_17AAG_DN KAAB_FAILED_HEART_VENTRICLE_DN ZAMORA_NOS2_TARGETS_UP GALLUZZI_PERMEABILIZE_MITOCHONDRIA HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5 STEIN_ESR1_TARGETS PAL_PRMT5_TARGETS_DN SWEET_LUNG_CANCER_KRAS_UP YANAGIHARA_ESX1_TARGETS
MPEA 0.000 0.0002 0.0002 0.0004 0.0008 0.0015 0.0017 0.0026 0.0039 0.0044 0.0054 0.0054 0.0066 0.0069 0.0074 0.0075 0.0075 0.0079 0.0089 0.0102 0.0112 0.0112 0.0121 0.0129 0.0154 0.0167 0.0169 0.0169 0.0170 0.0182 0.0189 0.0198 0.0199 0.0200 0.0203 0.0204 0.0205 0.0214 0.0244 0.0246 0.0247 0.0259 0.0262 0.0263 0.0271 0.0280 0.0283 0.0292 0.0305 0.0305 0.0311 0.0317 0.0319 0.032 0.0321 0.0323 0.0326 0.0337 0.0342 0.0342 0.0344 0.0352 0.0358 0.0359 0.0362 0.0369 0.0392 0.0392 0.0400 0.0402 0.0404 0.0408 0.0412 0.0413 0.0416 0.0421 0.0424 0.0431 0.0433 0.0433 0.0440 0.0453 0.0463 0.0464 0.0466 0.0469 0.0483 0.0484 0.0492
GSEA 0.291 0.9327 0.0598 0.1691 0.7956 0.1772 0.0900 0.5780 0.4619 0.4133 0.2218 0.0718 0.5468 0.0696 0.8420 0.3342 0.5169 0.1087 0.3947 0.7628 0.5228 0.5824 0.7770 0.1379 0.0698 0.1412 0.1897 0.0973 0.4608 0.1388 0.2127 0.2207 0.7351 0.1453 0.4514 0.4100 0.1710 0.1416 0.0612 0.5963 0.5058 0.1657 0.1718 0.1178 0.9480 0.1467 0.1546 0.1377 0.0933 0.1770 0.7882 0.6031 0.5332 0.605 0.3370 0.6280 0.2602 0.6960 0.3417 0.2365 0.7404 0.1219 0.1604 0.5501 0.4547 0.4536 0.1674 0.1073 0.6393 0.6722 0.5114 0.3243 0.3485 0.1028 0.6909 0.4692 0.2258 0.2039 0.5153 0.1194 0.3925 0.2875 0.0842 0.3022 0.7105 0.1241 0.3388 0.2717 0.2867

Identifying the pathways significant in GSEA not in MPEA

Significant_in_GSEA_not_in_dcor <- setdiff(rownames(gsea_results_significant),Mutually_identified_in_GSEA_dcor)
pvalue_of_disparities <- rbind(nominal_dcor_pvalues[Significant_in_GSEA_not_in_dcor],gsea_results[Significant_in_GSEA_not_in_dcor,]$NOM.p.val)
rownames(pvalue_of_disparities) <- c("MPEA","GSEA")
pvalue_of_disparities %>%
  kable("html", digits = 4, longtable = TRUE) %>%
  kable_styling(bootstrap_options = "striped", font_size = 12, full_width = F) %>%
  row_spec(0, angle = -0)
REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS BIOCARTA_BAD_PATHWAY REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION WINNEPENNINCKX_MELANOMA_METASTASIS_DN BIOCARTA_CSK_PATHWAY VERRECCHIA_RESPONSE_TO_TGFB1_C1 RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN QI_HYPOXIA WINTER_HYPOXIA_METAGENE BROWNE_HCMV_INFECTION_2HR_DN KARLSSON_TGFB1_TARGETS_UP SEIDEN_ONCOGENESIS_BY_MET ANDERSEN_CHOLANGIOCARCINOMA_CLASS2 SEMENZA_HIF1_TARGETS DAZARD_UV_RESPONSE_CLUSTER_G1 LANDIS_BREAST_CANCER_PROGRESSION_UP ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN MENSE_HYPOXIA_UP KIM_WT1_TARGETS_12HR_DN TOOKER_GEMCITABINE_RESISTANCE_DN REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM YANG_BREAST_CANCER_ESR1_LASER_DN KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3 KRIEG_HYPOXIA_NOT_VIA_KDM3A ELVIDGE_HYPOXIA_BY_DMOG_UP WINTER_HYPOXIA_UP RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP CHEN_LUNG_CANCER_SURVIVAL SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2 BHATTACHARYA_EMBRYONIC_STEM_CELL BIOCARTA_VEGF_PATHWAY PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN LEE_DIFFERENTIATING_T_LYMPHOCYTE REACTOME_PLC_BETA_MEDIATED_EVENTS REACTOME_OPIOID_SIGNALLING BIOCARTA_IL12_PATHWAY KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS BERENJENO_TRANSFORMED_BY_RHOA_UP REACTOME_AQUAPORIN_MEDIATED_TRANSPORT BIOCARTA_HCMV_PATHWAY CHIN_BREAST_CANCER_COPY_NUMBER_UP HARRIS_HYPOXIA YU_MYC_TARGETS_DN REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE FURUKAWA_DUSP6_TARGETS_PCI35_DN WINTER_HYPOXIA_DN KEGG_CHRONIC_MYELOID_LEUKEMIA PID_TCR_PATHWAY VECCHI_GASTRIC_CANCER_EARLY_UP RAMALHO_STEMNESS_UP REACTOME_TRNA_AMINOACYLATION PRAMOONJAGO_SOX4_TARGETS_UP SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6 SENESE_HDAC2_TARGETS_UP KEGG_BLADDER_CANCER SCHUHMACHER_MYC_TARGETS_UP KEGG_AMINOACYL_TRNA_BIOSYNTHESIS REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1 REACTOME_DAG_AND_IP3_SIGNALING IVANOVSKA_MIR106B_TARGETS BIOCARTA_RAS_PATHWAY SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP CROMER_METASTASIS_DN AMIT_EGF_RESPONSE_480_MCF10A MURAKAMI_UV_RESPONSE_6HR_UP LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP LU_EZH2_TARGETS_DN SESTO_RESPONSE_TO_UV_C2 MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN BIOCARTA_CXCR4_PATHWAY BILD_MYC_ONCOGENIC_SIGNATURE SMID_BREAST_CANCER_NORMAL_LIKE_UP LEE_CALORIE_RESTRICTION_NEOCORTEX_DN REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS LEONARD_HYPOXIA COLLER_MYC_TARGETS_UP BIOCARTA_MTOR_PATHWAY KEGG_TASTE_TRANSDUCTION SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN SENESE_HDAC1_TARGETS_UP SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN ELVIDGE_HIF1A_TARGETS_DN NAKAMURA_CANCER_MICROENVIRONMENT_DN PID_DELTA_NP63_PATHWAY BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN REACTOME_IL1_SIGNALING SWEET_KRAS_ONCOGENIC_SIGNATURE ELVIDGE_HYPOXIA_UP MANALO_HYPOXIA_UP WILLERT_WNT_SIGNALING PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4 LIAO_METASTASIS BLUM_RESPONSE_TO_SALIRASIB_UP AMIT_EGF_RESPONSE_480_HELA BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN GROSS_HYPOXIA_VIA_ELK3_DN KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION BASAKI_YBX1_TARGETS_UP REACTOME_CA_DEPENDENT_EVENTS WANG_SMARCE1_TARGETS_DN SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN WEI_MYCN_TARGETS_WITH_E_BOX PID_A6B1_A6B4_INTEGRIN_PATHWAY STARK_HYPPOCAMPUS_22Q11_DELETION_UP GENTILE_RESPONSE_CLUSTER_D3 PID_MTOR_4PATHWAY DANG_REGULATED_BY_MYC_UP LI_AMPLIFIED_IN_LUNG_CANCER LEI_MYB_TARGETS REACTOME_METABOLISM_OF_NUCLEOTIDES BIOCARTA_RACCYCD_PATHWAY SMID_BREAST_CANCER_BASAL_UP COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP SMITH_TERT_TARGETS_UP ALONSO_METASTASIS_EMT_UP GRANDVAUX_IRF3_TARGETS_DN KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM REACTOME_PI_METABOLISM ZHAN_MULTIPLE_MYELOMA_CD2_DN CAFFAREL_RESPONSE_TO_THC_24HR_5_UP NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON SMIRNOV_RESPONSE_TO_IR_2HR_DN KEGG_ERBB_SIGNALING_PATHWAY ZUCCHI_METASTASIS_DN ZHOU_TNF_SIGNALING_30MIN PID_TAP63_PATHWAY KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN REACTOME_PYRIMIDINE_METABOLISM NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN HOFMANN_CELL_LYMPHOMA_UP BIOCARTA_FMLP_PATHWAY PID_MYC_ACTIV_PATHWAY CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN MOOTHA_GLUCONEOGENESIS PID_EPHB_FWD_PATHWAY KIM_WT1_TARGETS_8HR_UP PID_UPA_UPAR_PATHWAY SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS FARMER_BREAST_CANCER_BASAL_VS_LULMINAL BHAT_ESR1_TARGETS_VIA_AKT1_UP SHEPARD_CRUSH_AND_BURN_MUTANT_UP NUYTTEN_NIPP1_TARGETS_UP DOANE_BREAST_CANCER_CLASSES_DN SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE CLIMENT_BREAST_CANCER_COPY_NUMBER_UP THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP SANA_RESPONSE_TO_IFNG_DN KEGG_PYRIMIDINE_METABOLISM KIM_WT1_TARGETS_UP ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF FRIDMAN_IMMORTALIZATION_DN PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7 ZHAN_MULTIPLE_MYELOMA_PR_UP PHONG_TNF_RESPONSE_VIA_P38_PARTIAL BIOCARTA_SPPA_PATHWAY JIANG_HYPOXIA_NORMAL WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN DAZARD_UV_RESPONSE_CLUSTER_G2 RICKMAN_HEAD_AND_NECK_CANCER_D CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN PID_CD8_TCR_PATHWAY GENTILE_UV_RESPONSE_CLUSTER_D5 BILD_HRAS_ONCOGENIC_SIGNATURE LIM_MAMMARY_STEM_CELL_DN DITTMER_PTHLH_TARGETS_UP LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT WHITFIELD_CELL_CYCLE_G2_M POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP PID_NCADHERIN_PATHWAY GENTILE_UV_RESPONSE_CLUSTER_D7 PID_HIF1_TFPATHWAY NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP GROSS_HYPOXIA_VIA_ELK3_ONLY_UP NEMETH_INFLAMMATORY_RESPONSE_LPS_UP LINDGREN_BLADDER_CANCER_CLUSTER_3_DN TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP NUYTTEN_NIPP1_TARGETS_DN SENESE_HDAC3_TARGETS_UP MORI_SMALL_PRE_BII_LYMPHOCYTE_DN PID_CERAMIDE_PATHWAY DORSAM_HOXA9_TARGETS_UP NATSUME_RESPONSE_TO_INTERFERON_BETA_DN WANG_LMO4_TARGETS_DN MOHANKUMAR_HOXA1_TARGETS_DN ONDER_CDH1_TARGETS_1_DN BENPORATH_MYC_TARGETS_WITH_EBOX FERNANDEZ_BOUND_BY_MYC GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP YAGI_AML_WITH_INV_16_TRANSLOCATION FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP LINSLEY_MIR16_TARGETS KEGG_ACUTE_MYELOID_LEUKEMIA HOELZEL_NF1_TARGETS_UP BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP KEGG_PATHWAYS_IN_CANCER BASSO_HAIRY_CELL_LEUKEMIA_UP REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN BRUINS_UVC_RESPONSE_LATE MARTINEZ_RB1_TARGETS_UP DOUGLAS_BMI1_TARGETS_UP ALFANO_MYC_TARGETS RAMALHO_STEMNESS_DN VANASSE_BCL2_TARGETS_DN REACTOME_DARPP_32_EVENTS CHANG_CORE_SERUM_RESPONSE_DN ST_G_ALPHA_I_PATHWAY REACTOME_RECYCLING_PATHWAY_OF_L1 WILENSKY_RESPONSE_TO_DARAPLADIB BORCZUK_MALIGNANT_MESOTHELIOMA_DN BIOCARTA_IL7_PATHWAY REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP PID_RAC1_REG_PATHWAY MIKKELSEN_IPS_WITH_HCP_H3K27ME3 ZHAN_MULTIPLE_MYELOMA_CD2_UP ROVERSI_GLIOMA_COPY_NUMBER_UP SCHLOSSER_SERUM_RESPONSE_UP FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP MIKKELSEN_IPS_ICP_WITH_H3K27ME3 REACTOME_G_PROTEIN_ACTIVATION REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS CORRE_MULTIPLE_MYELOMA_DN REACTOME_GLYCOSPHINGOLIPID_METABOLISM BIOCARTA_CTLA4_PATHWAY VECCHI_GASTRIC_CANCER_EARLY_DN REACTOME_INTEGRATION_OF_ENERGY_METABOLISM AKL_HTLV1_INFECTION_DN KATSANOU_ELAVL1_TARGETS_UP VALK_AML_WITH_FLT3_ITD LEIN_MIDBRAIN_MARKERS HUTTMANN_B_CLL_POOR_SURVIVAL_UP KEGG_GNRH_SIGNALING_PATHWAY LEE_LIVER_CANCER_SURVIVAL_UP LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES KEGG_MELANOGENESIS MA_MYELOID_DIFFERENTIATION_DN REACTOME_REGULATION_OF_INSULIN_SECRETION HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP GRADE_COLON_AND_RECTAL_CANCER_DN ST_ADRENERGIC CROMER_TUMORIGENESIS_DN PID_IL3_PATHWAY REACTOME_G_ALPHA_S_SIGNALLING_EVENTS CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY MCCLUNG_COCAINE_REWARD_5D REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION MCCLUNG_DELTA_FOSB_TARGETS_8WK NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN KONDO_PROSTATE_CANCER_WITH_H3K27ME3 SANSOM_APC_TARGETS_DN WNT_SIGNALING KASLER_HDAC7_TARGETS_1_UP REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY KEGG_GLYCEROPHOSPHOLIPID_METABOLISM PEREZ_TP53_TARGETS TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP PEREZ_TP63_TARGETS
MPEA 0.7378 0.5571 0.5781 0.2336 0.2743 0.3037 0.0761 0.0997 0.2149 0.0750 0.1620 0.8947 0.1020 0.0891 0.1534 0.3641 0.2668 0.1856 0.9176 0.6607 0.1265 0.286 0.5220 0.2893 0.268 0.2695 0.0564 0.4625 0.1741 0.2944 0.2293 0.2315 0.3597 0.1862 0.6008 0.6931 0.6419 0.0542 0.4035 0.0515 0.7286 0.0759 0.0579 0.3090 0.1584 0.7365 0.7886 0.0714 0.0723 0.8479 0.5169 0.2884 0.5786 0.8943 0.2648 0.4949 0.1011 0.0972 0.1694 0.8929 0.5817 0.7332 0.4657 0.8005 0.1148 0.2231 0.9986 0.2554 0.7102 0.5615 0.2025 0.5714 0.4260 0.9997 0.1820 0.8684 0.8024 0.4020 0.8034 0.1146 0.9698 0.9356 0.1459 0.9933 0.6897 0.7546 0.3694 0.2905 0.8757 0.2959 0.9911 0.3079 0.1854 0.3089 0.1144 0.9810 0.8755 0.9731 0.2279 0.4236 0.8676 0.2433 0.5499 0.7948 0.0868 0.1761 0.9459 0.2861 0.2832 0.3370 0.6310 0.2453 0.0709 0.0737 0.3087 0.6667 0.1466 0.1469 0.9065 0.3790 0.5266 0.8446 0.6033 0.0636 0.8586 0.2948 0.9103 0.1354 0.0613 0.4811 0.2623 0.6438 0.3242 0.0508 0.2102 0.7541 0.1961 0.6169 0.0562 0.8022 0.5121 0.6111 0.1176 0.2852 0.8856 0.9848 0.8985 0.1861 0.1331 0.1062 0.3902 0.1575 0.3426 0.7689 0.6075 0.4671 0.8618 0.3905 0.6833 0.6805 0.3967 0.4568 0.2503 0.2012 0.1441 0.8961 0.1235 0.8780 0.1719 0.0819 0.0728 0.9807 0.0526 0.5686 0.7035 0.2372 0.7971 0.5284 0.722 0.5458 0.3099 0.8987 0.1661 0.3209 0.5076 0.8819 0.7034 0.2284 0.9657 0.2203 0.7544 0.2850 0.0736 0.2230 0.6301 0.5829 0.7445 0.8445 0.3102 0.1377 0.8461 0.5774 0.7244 0.8964 0.0827 0.9957 0.9254 0.9651 0.6121 0.7684 0.9926 0.7093 0.7984 0.5049 0.2448 0.2112 0.8308 0.0510 0.2913 0.6929 0.9865 0.7825 0.7982 0.5034 0.2603 0.1376 0.3350 0.8724 0.7865 0.5926 0.8722 0.7125 0.3439 0.5457 0.5283 0.605 0.2805 0.9854 0.1286 0.8252 0.6748 0.8479 0.0555 0.7670 0.9271 0.4653 0.3027 0.9999 0.3101 0.0970 0.8599 0.8667 0.3382 0.0967 0.8227 0.6332 0.6905 0.7165 0.9925 0.3234 0.9817 0.5284 0.3226 0.1146 0.9212 0.2590 0.9993
GSEA 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0024 0.0000 0.0000 0.0045 0.0021 0.0000 0.0047 0.0000 0.0021 0.0066 0.0046 0.0042 0.0021 0.0021 0.0021 0.008 0.0023 0.0023 0.000 0.0022 0.0000 0.0020 0.0069 0.0022 0.0098 0.0041 0.0000 0.0000 0.0095 0.0000 0.0000 0.0130 0.0084 0.0150 0.0018 0.0041 0.0115 0.0114 0.0098 0.0000 0.0018 0.0261 0.0060 0.0041 0.0000 0.0188 0.0140 0.0308 0.0150 0.0465 0.0092 0.0093 0.0267 0.0308 0.0052 0.0000 0.0174 0.0085 0.0262 0.0193 0.0116 0.0128 0.0203 0.0130 0.0142 0.0217 0.0221 0.0067 0.0167 0.0023 0.0073 0.0247 0.0251 0.0098 0.0034 0.0123 0.0020 0.0161 0.0023 0.0229 0.0114 0.0394 0.0046 0.0249 0.0130 0.0232 0.0112 0.0088 0.0100 0.0182 0.0113 0.0087 0.0211 0.0104 0.0118 0.0072 0.0196 0.0018 0.0047 0.0397 0.0131 0.0147 0.0018 0.0343 0.0165 0.0269 0.0172 0.0022 0.0147 0.0263 0.0026 0.0183 0.0288 0.0466 0.0346 0.0444 0.0251 0.0341 0.0424 0.0363 0.0263 0.0044 0.0398 0.0286 0.0292 0.0219 0.0199 0.0141 0.0221 0.0305 0.0375 0.0335 0.0309 0.0198 0.0252 0.0355 0.0432 0.0000 0.0024 0.0179 0.0117 0.0381 0.0165 0.0252 0.0303 0.0438 0.0437 0.0279 0.0435 0.0461 0.0219 0.0420 0.0376 0.0291 0.0129 0.0345 0.0424 0.0067 0.0345 0.0144 0.0365 0.0273 0.0459 0.0455 0.0412 0.0462 0.0053 0.0390 0.0428 0.0402 0.0279 0.0420 0.044 0.0254 0.0330 0.0168 0.0291 0.0203 0.0488 0.0473 0.0337 0.0499 0.0327 0.0341 0.0340 0.0162 0.0164 0.0115 0.0218 0.0205 0.0480 0.0396 0.0465 0.0482 0.0477 0.0302 0.0394 0.0071 0.0350 0.0383 0.0134 0.0467 0.0477 0.0128 0.0035 0.0096 0.0167 0.0053 0.0196 0.0251 0.0181 0.0366 0.0190 0.0346 0.0176 0.0378 0.0252 0.0401 0.0368 0.0187 0.0245 0.0251 0.0297 0.0343 0.0137 0.0443 0.0462 0.0370 0.0283 0.049 0.0486 0.0491 0.0433 0.0468 0.0394 0.0334 0.0399 0.0304 0.0455 0.0407 0.0323 0.0383 0.0455 0.0433 0.0478 0.0411 0.0414 0.0243 0.0396 0.0491 0.0322 0.0444 0.0291 0.0337 0.0255 0.0255 0.0407 0.0360 0.0162 0.0349 0.0339

Close cluster

# stopCluster(cl)

PCA plot of pathways deemed significant in MPEA but not GSEA

library(ggfortify)
## Loading required package: ggplot2
for (name in (sort(Significant_in_dcor_not_in_GSEA, decreasing = F))){
strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
genotypes_category <- as.data.frame(genotypes_category)
print(name)
print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()) 

# pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
# biplot.pcoa(pcoa.obj)
}
## [1] "ABE_VEGFA_TARGETS_2HR"

## [1] "ABE_VEGFA_TARGETS_30MIN"

## [1] "ANDERSEN_LIVER_CANCER_KRT19_UP"

## [1] "APPIERTO_RESPONSE_TO_FENRETINIDE_DN"

## [1] "BENPORATH_PROLIFERATION"

## [1] "BOYAULT_LIVER_CANCER_SUBCLASS_G5_DN"

## [1] "BOYLAN_MULTIPLE_MYELOMA_D_DN"

## [1] "BOYLAN_MULTIPLE_MYELOMA_PCA1_UP"

## [1] "BROWNE_HCMV_INFECTION_2HR_UP"

## [1] "CHIANG_LIVER_CANCER_SUBCLASS_PROLIFERATION_UP"

## [1] "CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_CDC25_UP"

## [1] "CONCANNON_APOPTOSIS_BY_EPOXOMICIN_DN"

## [1] "DAVIES_MULTIPLE_MYELOMA_VS_MGUS_DN"

## [1] "DELPUECH_FOXO3_TARGETS_UP"

## [1] "DOANE_RESPONSE_TO_ANDROGEN_UP"

## [1] "DORN_ADENOVIRUS_INFECTION_12HR_UP"

## [1] "DORN_ADENOVIRUS_INFECTION_48HR_DN"

## [1] "DORSAM_HOXA9_TARGETS_DN"

## [1] "DURAND_STROMA_NS_UP"

## [1] "GALLUZZI_PERMEABILIZE_MITOCHONDRIA"

## [1] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_UP"

## [1] "HAHTOLA_SEZARY_SYNDROM_UP"

## [1] "HAN_JNK_SINGALING_UP"

## [1] "HELLER_SILENCED_BY_METHYLATION_UP"

## [1] "HENDRICKS_SMARCA4_TARGETS_UP"

## [1] "HOFFMANN_SMALL_PRE_BII_TO_IMMATURE_B_LYMPHOCYTE_DN"

## [1] "HUPER_BREAST_BASAL_VS_LUMINAL_UP"

## [1] "ICHIBA_GRAFT_VERSUS_HOST_DISEASE_35D_UP"

## [1] "JIANG_AGING_CEREBRAL_CORTEX_DN"

## [1] "JOSEPH_RESPONSE_TO_SODIUM_BUTYRATE_UP"

## [1] "KAAB_FAILED_HEART_VENTRICLE_DN"

## [1] "KAMIKUBO_MYELOID_CEBPA_NETWORK"

## [1] "KEGG_CYSTEINE_AND_METHIONINE_METABOLISM"

## [1] "KEGG_PROPANOATE_METABOLISM"

## [1] "KEGG_PYRUVATE_METABOLISM"

## [1] "KIM_RESPONSE_TO_TSA_AND_DECITABINE_UP"

## [1] "KIM_TIAL1_TARGETS"

## [1] "KRIGE_RESPONSE_TO_TOSEDOSTAT_6HR_UP"

## [1] "KYNG_RESPONSE_TO_H2O2_VIA_ERCC6_UP"

## [1] "LEE_TARGETS_OF_PTCH1_AND_SUFU_DN"

## [1] "LINDVALL_IMMORTALIZED_BY_TERT_UP"

## [1] "MALONEY_RESPONSE_TO_17AAG_DN"

## [1] "MCDOWELL_ACUTE_LUNG_INJURY_UP"

## [1] "MEISSNER_BRAIN_HCP_WITH_H3K27ME3"

## [1] "MEISSNER_NPC_HCP_WITH_H3_UNMETHYLATED"

## [1] "MIKKELSEN_MEF_HCP_WITH_H3_UNMETHYLATED"

## [1] "MIYAGAWA_TARGETS_OF_EWSR1_ETS_FUSIONS_UP"

## [1] "MOREIRA_RESPONSE_TO_TSA_UP"

## [1] "MUELLER_METHYLATED_IN_GLIOBLASTOMA"

## [1] "NABA_MATRISOME_ASSOCIATED"

## [1] "NABA_SECRETED_FACTORS"

## [1] "NAKAJIMA_EOSINOPHIL"

## [1] "OUELLET_CULTURED_OVARIAN_CANCER_INVASIVE_VS_LMP_UP"

## [1] "PAL_PRMT5_TARGETS_DN"

## [1] "PANGAS_TUMOR_SUPPRESSION_BY_SMAD1_AND_SMAD5_UP"

## [1] "PARK_APL_PATHOGENESIS_DN"

## [1] "PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP"

## [1] "REACTOME_BMAL1_CLOCK_NPAS2_ACTIVATES_CIRCADIAN_EXPRESSION"

## [1] "REACTOME_PRE_NOTCH_EXPRESSION_AND_PROCESSING"

## [1] "REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE"

## [1] "ROSS_AML_WITH_PML_RARA_FUSION"

## [1] "SANA_TNF_SIGNALING_DN"

## [1] "SANSOM_APC_TARGETS_UP"

## [1] "SATO_SILENCED_EPIGENETICALLY_IN_PANCREATIC_CANCER"

## [1] "SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN"

## [1] "SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1"

## [1] "SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM5"

## [1] "SIMBULAN_UV_RESPONSE_NORMAL_DN"

## [1] "SMID_BREAST_CANCER_RELAPSE_IN_PLEURA_DN"

## [1] "STEARMAN_LUNG_CANCER_EARLY_VS_LATE_DN"

## [1] "STEARMAN_TUMOR_FIELD_EFFECT_UP"

## [1] "STEIN_ESR1_TARGETS"

## [1] "STEIN_ESRRA_TARGETS"

## [1] "SU_PLACENTA"

## [1] "SWEET_LUNG_CANCER_KRAS_UP"

## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_16D_DN"

## [1] "TSUNODA_CISPLATIN_RESISTANCE_DN"

## [1] "VANDESLUIS_COMMD1_TARGETS_GROUP_3_DN"

## [1] "VANDESLUIS_COMMD1_TARGETS_GROUP_3_UP"

## [1] "VANTVEER_BREAST_CANCER_METASTASIS_UP"

## [1] "WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_DN"

## [1] "WANG_BARRETTS_ESOPHAGUS_AND_ESOPHAGUS_CANCER_UP"

## [1] "WANG_BARRETTS_ESOPHAGUS_UP"

## [1] "YAMAZAKI_TCEB3_TARGETS_DN"

## [1] "YANAGIHARA_ESX1_TARGETS"

## [1] "YAO_TEMPORAL_RESPONSE_TO_PROGESTERONE_CLUSTER_9"

## [1] "ZAMORA_NOS2_TARGETS_UP"

## [1] "ZHAN_MULTIPLE_MYELOMA_DN"

## [1] "ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN"

PCA plot of pathways deemed significant in GSEA but not MPEA

rownames(gsea_results_significant)
##   [1] "REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS"                             
##   [2] "BIOCARTA_BAD_PATHWAY"                                                                 
##   [3] "REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION"                                  
##   [4] "WINNEPENNINCKX_MELANOMA_METASTASIS_DN"                                                
##   [5] "BIOCARTA_CSK_PATHWAY"                                                                 
##   [6] "VERRECCHIA_RESPONSE_TO_TGFB1_C1"                                                      
##   [7] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN"                                   
##   [8] "QI_HYPOXIA"                                                                           
##   [9] "WINTER_HYPOXIA_METAGENE"                                                              
##  [10] "LI_LUNG_CANCER"                                                                       
##  [11] "BROWNE_HCMV_INFECTION_2HR_DN"                                                         
##  [12] "KARLSSON_TGFB1_TARGETS_UP"                                                            
##  [13] "SEIDEN_ONCOGENESIS_BY_MET"                                                            
##  [14] "ANDERSEN_CHOLANGIOCARCINOMA_CLASS2"                                                   
##  [15] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_POORLY_DN"                                       
##  [16] "SEMENZA_HIF1_TARGETS"                                                                 
##  [17] "DAZARD_UV_RESPONSE_CLUSTER_G1"                                                        
##  [18] "GU_PDEF_TARGETS_DN"                                                                   
##  [19] "LANDIS_BREAST_CANCER_PROGRESSION_UP"                                                  
##  [20] "ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN"                                                   
##  [21] "MENSE_HYPOXIA_UP"                                                                     
##  [22] "KIM_WT1_TARGETS_12HR_DN"                                                              
##  [23] "TOOKER_GEMCITABINE_RESISTANCE_DN"                                                     
##  [24] "ENK_UV_RESPONSE_EPIDERMIS_UP"                                                         
##  [25] "REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS"                                        
##  [26] "SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM"                                             
##  [27] "YANG_BREAST_CANCER_ESR1_LASER_DN"                                                     
##  [28] "KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3"                                                    
##  [29] "KRIEG_HYPOXIA_NOT_VIA_KDM3A"                                                          
##  [30] "ELVIDGE_HYPOXIA_BY_DMOG_UP"                                                           
##  [31] "WINTER_HYPOXIA_UP"                                                                    
##  [32] "RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP"                                            
##  [33] "CHEN_LUNG_CANCER_SURVIVAL"                                                            
##  [34] "KEGG_GLYCOLYSIS_GLUCONEOGENESIS"                                                      
##  [35] "SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE"                               
##  [36] "PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2"                                          
##  [37] "BHATTACHARYA_EMBRYONIC_STEM_CELL"                                                     
##  [38] "BIOCARTA_VEGF_PATHWAY"                                                                
##  [39] "MARTORIATI_MDM4_TARGETS_NEUROEPITHELIUM_UP"                                           
##  [40] "HOFFMANN_IMMATURE_TO_MATURE_B_LYMPHOCYTE_UP"                                          
##  [41] "PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN"                                                  
##  [42] "LEE_DIFFERENTIATING_T_LYMPHOCYTE"                                                     
##  [43] "REACTOME_PLC_BETA_MEDIATED_EVENTS"                                                    
##  [44] "REACTOME_OPIOID_SIGNALLING"                                                           
##  [45] "BIOCARTA_IL12_PATHWAY"                                                                
##  [46] "KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"                                                  
##  [47] "BERENJENO_TRANSFORMED_BY_RHOA_UP"                                                     
##  [48] "REACTOME_AQUAPORIN_MEDIATED_TRANSPORT"                                                
##  [49] "BIOCARTA_HCMV_PATHWAY"                                                                
##  [50] "CHIN_BREAST_CANCER_COPY_NUMBER_UP"                                                    
##  [51] "HARRIS_HYPOXIA"                                                                       
##  [52] "YU_MYC_TARGETS_DN"                                                                    
##  [53] "REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS"                                         
##  [54] "REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE"                                            
##  [55] "FURUKAWA_DUSP6_TARGETS_PCI35_DN"                                                      
##  [56] "WINTER_HYPOXIA_DN"                                                                    
##  [57] "KEGG_CHRONIC_MYELOID_LEUKEMIA"                                                        
##  [58] "PID_TCR_PATHWAY"                                                                      
##  [59] "VECCHI_GASTRIC_CANCER_EARLY_UP"                                                       
##  [60] "RAMALHO_STEMNESS_UP"                                                                  
##  [61] "REACTOME_TRNA_AMINOACYLATION"                                                         
##  [62] "PRAMOONJAGO_SOX4_TARGETS_UP"                                                          
##  [63] "SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6"                                                 
##  [64] "SENESE_HDAC2_TARGETS_UP"                                                              
##  [65] "KEGG_BLADDER_CANCER"                                                                  
##  [66] "SCHUHMACHER_MYC_TARGETS_UP"                                                           
##  [67] "KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"                                                     
##  [68] "REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1"                   
##  [69] "REACTOME_DAG_AND_IP3_SIGNALING"                                                       
##  [70] "IVANOVSKA_MIR106B_TARGETS"                                                            
##  [71] "KIM_HYPOXIA"                                                                          
##  [72] "BIOCARTA_RAS_PATHWAY"                                                                 
##  [73] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP"                                                
##  [74] "CROMER_METASTASIS_DN"                                                                 
##  [75] "AMIT_EGF_RESPONSE_480_MCF10A"                                                         
##  [76] "MURAKAMI_UV_RESPONSE_6HR_UP"                                                          
##  [77] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP"                                
##  [78] "LU_EZH2_TARGETS_DN"                                                                   
##  [79] "SESTO_RESPONSE_TO_UV_C2"                                                              
##  [80] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN"                                                  
##  [81] "BIOCARTA_CXCR4_PATHWAY"                                                               
##  [82] "BILD_MYC_ONCOGENIC_SIGNATURE"                                                         
##  [83] "GRAESSMANN_RESPONSE_TO_MC_AND_SERUM_DEPRIVATION_DN"                                   
##  [84] "SMID_BREAST_CANCER_NORMAL_LIKE_UP"                                                    
##  [85] "LEE_CALORIE_RESTRICTION_NEOCORTEX_DN"                                                 
##  [86] "REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS"                                              
##  [87] "LEONARD_HYPOXIA"                                                                      
##  [88] "COLLER_MYC_TARGETS_UP"                                                                
##  [89] "BIOCARTA_MTOR_PATHWAY"                                                                
##  [90] "KEGG_TASTE_TRANSDUCTION"                                                              
##  [91] "JAEGER_METASTASIS_DN"                                                                 
##  [92] "SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP"                                          
##  [93] "KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN"                                                   
##  [94] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN"                                         
##  [95] "SENESE_HDAC1_TARGETS_UP"                                                              
##  [96] "SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN"                                                 
##  [97] "ELVIDGE_HIF1A_TARGETS_DN"                                                             
##  [98] "CHIARADONNA_NEOPLASTIC_TRANSFORMATION_KRAS_UP"                                        
##  [99] "NAKAMURA_CANCER_MICROENVIRONMENT_DN"                                                  
## [100] "PID_DELTA_NP63_PATHWAY"                                                               
## [101] "MARTORIATI_MDM4_TARGETS_FETAL_LIVER_UP"                                               
## [102] "COLDREN_GEFITINIB_RESISTANCE_DN"                                                      
## [103] "BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN"                                             
## [104] "REACTOME_IL1_SIGNALING"                                                               
## [105] "SWEET_KRAS_ONCOGENIC_SIGNATURE"                                                       
## [106] "ELVIDGE_HYPOXIA_UP"                                                                   
## [107] "MANALO_HYPOXIA_UP"                                                                    
## [108] "BIOCARTA_CERAMIDE_PATHWAY"                                                            
## [109] "WILLERT_WNT_SIGNALING"                                                                
## [110] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4"                                               
## [111] "LIAO_METASTASIS"                                                                      
## [112] "BLUM_RESPONSE_TO_SALIRASIB_UP"                                                        
## [113] "AMIT_EGF_RESPONSE_480_HELA"                                                           
## [114] "BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN"                                              
## [115] "VANTVEER_BREAST_CANCER_ESR1_DN"                                                       
## [116] "GROSS_HYPOXIA_VIA_ELK3_DN"                                                            
## [117] "KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"                                        
## [118] "BASAKI_YBX1_TARGETS_UP"                                                               
## [119] "REACTOME_CA_DEPENDENT_EVENTS"                                                         
## [120] "WANG_SMARCE1_TARGETS_DN"                                                              
## [121] "SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN"                                          
## [122] "WEI_MYCN_TARGETS_WITH_E_BOX"                                                          
## [123] "PID_A6B1_A6B4_INTEGRIN_PATHWAY"                                                       
## [124] "WU_CELL_MIGRATION"                                                                    
## [125] "STARK_HYPPOCAMPUS_22Q11_DELETION_UP"                                                  
## [126] "GENTILE_RESPONSE_CLUSTER_D3"                                                          
## [127] "PID_MTOR_4PATHWAY"                                                                    
## [128] "AMIT_SERUM_RESPONSE_480_MCF10A"                                                       
## [129] "HUPER_BREAST_BASAL_VS_LUMINAL_DN"                                                     
## [130] "DANG_REGULATED_BY_MYC_UP"                                                             
## [131] "LI_AMPLIFIED_IN_LUNG_CANCER"                                                          
## [132] "LEI_MYB_TARGETS"                                                                      
## [133] "REACTOME_METABOLISM_OF_NUCLEOTIDES"                                                   
## [134] "BIOCARTA_RACCYCD_PATHWAY"                                                             
## [135] "SESTO_RESPONSE_TO_UV_C1"                                                              
## [136] "SMID_BREAST_CANCER_BASAL_UP"                                                          
## [137] "COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP"                                                
## [138] "SMITH_TERT_TARGETS_UP"                                                                
## [139] "ALONSO_METASTASIS_EMT_UP"                                                             
## [140] "GRANDVAUX_IRF3_TARGETS_DN"                                                            
## [141] "KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"                                      
## [142] "REACTOME_PI_METABOLISM"                                                               
## [143] "ZHAN_MULTIPLE_MYELOMA_CD2_DN"                                                         
## [144] "CAFFAREL_RESPONSE_TO_THC_24HR_5_UP"                                                   
## [145] "SABATES_COLORECTAL_ADENOMA_UP"                                                        
## [146] "NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON"                                            
## [147] "SMIRNOV_RESPONSE_TO_IR_2HR_DN"                                                        
## [148] "KEGG_ERBB_SIGNALING_PATHWAY"                                                          
## [149] "ZUCCHI_METASTASIS_DN"                                                                 
## [150] "ZHOU_TNF_SIGNALING_30MIN"                                                             
## [151] "PID_TAP63_PATHWAY"                                                                    
## [152] "KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN"                                            
## [153] "REACTOME_PYRIMIDINE_METABOLISM"                                                       
## [154] "NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN"                                         
## [155] "HOFMANN_CELL_LYMPHOMA_UP"                                                             
## [156] "BIOCARTA_FMLP_PATHWAY"                                                                
## [157] "PID_MYC_ACTIV_PATHWAY"                                                                
## [158] "GAJATE_RESPONSE_TO_TRABECTEDIN_UP"                                                    
## [159] "CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN"                                            
## [160] "MOOTHA_GLUCONEOGENESIS"                                                               
## [161] "PID_EPHB_FWD_PATHWAY"                                                                 
## [162] "KIM_WT1_TARGETS_8HR_UP"                                                               
## [163] "PID_UPA_UPAR_PATHWAY"                                                                 
## [164] "SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS"                                           
## [165] "HAHTOLA_CTCL_CUTANEOUS"                                                               
## [166] "FARMER_BREAST_CANCER_BASAL_VS_LULMINAL"                                               
## [167] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"                                                        
## [168] "SHEPARD_CRUSH_AND_BURN_MUTANT_UP"                                                     
## [169] "NUYTTEN_NIPP1_TARGETS_UP"                                                             
## [170] "BAE_BRCA1_TARGETS_UP"                                                                 
## [171] "DOANE_BREAST_CANCER_CLASSES_DN"                                                       
## [172] "SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE"                                       
## [173] "CLIMENT_BREAST_CANCER_COPY_NUMBER_UP"                                                 
## [174] "THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP"                                               
## [175] "SANA_RESPONSE_TO_IFNG_DN"                                                             
## [176] "KEGG_PYRIMIDINE_METABOLISM"                                                           
## [177] "KIM_WT1_TARGETS_UP"                                                                   
## [178] "ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF"                                             
## [179] "FRIDMAN_IMMORTALIZATION_DN"                                                           
## [180] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7"                                               
## [181] "ZHAN_MULTIPLE_MYELOMA_PR_UP"                                                          
## [182] "PHONG_TNF_RESPONSE_VIA_P38_PARTIAL"                                                   
## [183] "BIOCARTA_SPPA_PATHWAY"                                                                
## [184] "JIANG_HYPOXIA_NORMAL"                                                                 
## [185] "WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN"                                    
## [186] "DAZARD_UV_RESPONSE_CLUSTER_G2"                                                        
## [187] "RICKMAN_HEAD_AND_NECK_CANCER_D"                                                       
## [188] "CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN"                                                
## [189] "PID_CD8_TCR_PATHWAY"                                                                  
## [190] "GENTILE_UV_RESPONSE_CLUSTER_D5"                                                       
## [191] "BILD_HRAS_ONCOGENIC_SIGNATURE"                                                        
## [192] "LIM_MAMMARY_STEM_CELL_DN"                                                             
## [193] "DITTMER_PTHLH_TARGETS_UP"                                                             
## [194] "WOOD_EBV_EBNA1_TARGETS_DN"                                                            
## [195] "LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT"                                               
## [196] "WHITFIELD_CELL_CYCLE_G2_M"                                                            
## [197] "POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP"                                                 
## [198] "PID_NCADHERIN_PATHWAY"                                                                
## [199] "GENTILE_UV_RESPONSE_CLUSTER_D7"                                                       
## [200] "PID_HIF1_TFPATHWAY"                                                                   
## [201] "ONDER_CDH1_TARGETS_2_DN"                                                              
## [202] "NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP"                                             
## [203] "GROSS_HYPOXIA_VIA_ELK3_ONLY_UP"                                                       
## [204] "NEMETH_INFLAMMATORY_RESPONSE_LPS_UP"                                                  
## [205] "LINDGREN_BLADDER_CANCER_CLUSTER_3_DN"                                                 
## [206] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP"                                    
## [207] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP"                                              
## [208] "NUYTTEN_NIPP1_TARGETS_DN"                                                             
## [209] "SENESE_HDAC3_TARGETS_UP"                                                              
## [210] "MORI_SMALL_PRE_BII_LYMPHOCYTE_DN"                                                     
## [211] "PID_CERAMIDE_PATHWAY"                                                                 
## [212] "DORSAM_HOXA9_TARGETS_UP"                                                              
## [213] "NATSUME_RESPONSE_TO_INTERFERON_BETA_DN"                                               
## [214] "LEE_LIVER_CANCER_ACOX1_UP"                                                            
## [215] "WANG_LMO4_TARGETS_DN"                                                                 
## [216] "MOHANKUMAR_HOXA1_TARGETS_DN"                                                          
## [217] "ONDER_CDH1_TARGETS_1_DN"                                                              
## [218] "BENPORATH_MYC_TARGETS_WITH_EBOX"                                                      
## [219] "FERNANDEZ_BOUND_BY_MYC"                                                               
## [220] "GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN"                                     
## [221] "KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP"                                            
## [222] "YAGI_AML_WITH_INV_16_TRANSLOCATION"                                                   
## [223] "HAN_SATB1_TARGETS_UP"                                                                 
## [224] "FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP"                                       
## [225] "LINSLEY_MIR16_TARGETS"                                                                
## [226] "KEGG_ACUTE_MYELOID_LEUKEMIA"                                                          
## [227] "HOELZEL_NF1_TARGETS_UP"                                                               
## [228] "BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP"                                                    
## [229] "KEGG_PATHWAYS_IN_CANCER"                                                              
## [230] "BASSO_HAIRY_CELL_LEUKEMIA_UP"                                                         
## [231] "REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS"                                                 
## [232] "GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN"                                         
## [233] "FARMER_BREAST_CANCER_APOCRINE_VS_LUMINAL"                                             
## [234] "BRUINS_UVC_RESPONSE_LATE"                                                             
## [235] "MARTINEZ_RB1_TARGETS_UP"                                                              
## [236] "DOUGLAS_BMI1_TARGETS_UP"                                                              
## [237] "ALFANO_MYC_TARGETS"                                                                   
## [238] "RAMALHO_STEMNESS_DN"                                                                  
## [239] "VANASSE_BCL2_TARGETS_DN"                                                              
## [240] "REACTOME_DARPP_32_EVENTS"                                                             
## [241] "CHANG_CORE_SERUM_RESPONSE_DN"                                                         
## [242] "ST_G_ALPHA_I_PATHWAY"                                                                 
## [243] "REACTOME_RECYCLING_PATHWAY_OF_L1"                                                     
## [244] "WILENSKY_RESPONSE_TO_DARAPLADIB"                                                      
## [245] "BORCZUK_MALIGNANT_MESOTHELIOMA_DN"                                                    
## [246] "BIOCARTA_IL7_PATHWAY"                                                                 
## [247] "REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION"                                           
## [248] "REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL"    
## [249] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP"                                   
## [250] "PID_RAC1_REG_PATHWAY"                                                                 
## [251] "MIKKELSEN_IPS_WITH_HCP_H3K27ME3"                                                      
## [252] "ZHAN_MULTIPLE_MYELOMA_CD2_UP"                                                         
## [253] "ROVERSI_GLIOMA_COPY_NUMBER_UP"                                                        
## [254] "JIANG_AGING_HYPOTHALAMUS_DN"                                                          
## [255] "SCHLOSSER_SERUM_RESPONSE_UP"                                                          
## [256] "FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP"                                                
## [257] "MIKKELSEN_IPS_ICP_WITH_H3K27ME3"                                                      
## [258] "REACTOME_G_PROTEIN_ACTIVATION"                                                        
## [259] "REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS"
## [260] "CORRE_MULTIPLE_MYELOMA_DN"                                                            
## [261] "REACTOME_GLYCOSPHINGOLIPID_METABOLISM"                                                
## [262] "BIOCARTA_CTLA4_PATHWAY"                                                               
## [263] "VECCHI_GASTRIC_CANCER_EARLY_DN"                                                       
## [264] "REACTOME_INTEGRATION_OF_ENERGY_METABOLISM"                                            
## [265] "AKL_HTLV1_INFECTION_DN"                                                               
## [266] "KATSANOU_ELAVL1_TARGETS_UP"                                                           
## [267] "VALK_AML_WITH_FLT3_ITD"                                                               
## [268] "LEIN_MIDBRAIN_MARKERS"                                                                
## [269] "HUTTMANN_B_CLL_POOR_SURVIVAL_UP"                                                      
## [270] "KEGG_GNRH_SIGNALING_PATHWAY"                                                          
## [271] "LEE_LIVER_CANCER_SURVIVAL_UP"                                                         
## [272] "LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES"                                                 
## [273] "KEGG_MELANOGENESIS"                                                                   
## [274] "MA_MYELOID_DIFFERENTIATION_DN"                                                        
## [275] "REACTOME_REGULATION_OF_INSULIN_SECRETION"                                             
## [276] "HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP"                                                 
## [277] "GRADE_COLON_AND_RECTAL_CANCER_DN"                                                     
## [278] "ST_ADRENERGIC"                                                                        
## [279] "CROMER_TUMORIGENESIS_DN"                                                              
## [280] "PID_IL3_PATHWAY"                                                                      
## [281] "REACTOME_G_ALPHA_S_SIGNALLING_EVENTS"                                                 
## [282] "CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY"                                                
## [283] "MCCLUNG_COCAINE_REWARD_5D"                                                            
## [284] "REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR"                                      
## [285] "ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION"                                                   
## [286] "MCCLUNG_DELTA_FOSB_TARGETS_8WK"                                                       
## [287] "NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN"                                                  
## [288] "KONDO_PROSTATE_CANCER_WITH_H3K27ME3"                                                  
## [289] "SANSOM_APC_TARGETS_DN"                                                                
## [290] "WNT_SIGNALING"                                                                        
## [291] "KASLER_HDAC7_TARGETS_1_UP"                                                            
## [292] "REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY"                                            
## [293] "KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"                                                  
## [294] "PEREZ_TP53_TARGETS"                                                                   
## [295] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP"                                          
## [296] "PEREZ_TP63_TARGETS"
for (name in (Significant_in_GSEA_not_in_dcor)){
  strongestpathwaydcor <- unname(unlist(pathway_collapsed[name]))
  expressions_pathway <- as.data.frame(expressions[,which(colnames(expressions)%in% strongestpathwaydcor)])
  genotypes_category <- ifelse(genotypes==1, "MUT", "WT")
  genotypes_category <- as.data.frame(genotypes_category)
  print(name)
  print(autoplot(prcomp(expressions_pathway), data = genotypes_category, colour='genotypes_category' )+theme_bw()+ggtitle(label = "name")) 
  
  # pcoa.obj <- pcoa(D = dist(expressions_pathway), correction="none", rn=NULL)
  # biplot.pcoa(pcoa.obj)
}
## [1] "REACTOME_REGULATION_OF_WATER_BALANCE_BY_RENAL_AQUAPORINS"

## [1] "BIOCARTA_BAD_PATHWAY"

## [1] "REACTOME_GLUCAGON_SIGNALING_IN_METABOLIC_REGULATION"

## [1] "WINNEPENNINCKX_MELANOMA_METASTASIS_DN"

## [1] "BIOCARTA_CSK_PATHWAY"

## [1] "VERRECCHIA_RESPONSE_TO_TGFB1_C1"

## [1] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_DN"

## [1] "QI_HYPOXIA"

## [1] "WINTER_HYPOXIA_METAGENE"

## [1] "BROWNE_HCMV_INFECTION_2HR_DN"

## [1] "KARLSSON_TGFB1_TARGETS_UP"

## [1] "SEIDEN_ONCOGENESIS_BY_MET"

## [1] "ANDERSEN_CHOLANGIOCARCINOMA_CLASS2"

## [1] "SEMENZA_HIF1_TARGETS"

## [1] "DAZARD_UV_RESPONSE_CLUSTER_G1"

## [1] "LANDIS_BREAST_CANCER_PROGRESSION_UP"

## [1] "ELVIDGE_HIF1A_AND_HIF2A_TARGETS_DN"

## [1] "MENSE_HYPOXIA_UP"

## [1] "KIM_WT1_TARGETS_12HR_DN"

## [1] "TOOKER_GEMCITABINE_RESISTANCE_DN"

## [1] "REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS"

## [1] "SCHLOSSER_MYC_TARGETS_REPRESSED_BY_SERUM"

## [1] "YANG_BREAST_CANCER_ESR1_LASER_DN"

## [1] "KOINUMA_TARGETS_OF_SMAD2_OR_SMAD3"

## [1] "KRIEG_HYPOXIA_NOT_VIA_KDM3A"

## [1] "ELVIDGE_HYPOXIA_BY_DMOG_UP"

## [1] "WINTER_HYPOXIA_UP"

## [1] "RODRIGUES_THYROID_CARCINOMA_ANAPLASTIC_UP"

## [1] "CHEN_LUNG_CANCER_SURVIVAL"

## [1] "SHAFFER_IRF4_TARGETS_IN_MYELOMA_VS_MATURE_B_LYMPHOCYTE"

## [1] "PEDERSEN_TARGETS_OF_611CTF_ISOFORM_OF_ERBB2"

## [1] "BHATTACHARYA_EMBRYONIC_STEM_CELL"

## [1] "BIOCARTA_VEGF_PATHWAY"

## [1] "PASQUALUCCI_LYMPHOMA_BY_GC_STAGE_DN"

## [1] "LEE_DIFFERENTIATING_T_LYMPHOCYTE"

## [1] "REACTOME_PLC_BETA_MEDIATED_EVENTS"

## [1] "REACTOME_OPIOID_SIGNALLING"

## [1] "BIOCARTA_IL12_PATHWAY"

## [1] "KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS"

## [1] "BERENJENO_TRANSFORMED_BY_RHOA_UP"

## [1] "REACTOME_AQUAPORIN_MEDIATED_TRANSPORT"

## [1] "BIOCARTA_HCMV_PATHWAY"

## [1] "CHIN_BREAST_CANCER_COPY_NUMBER_UP"

## [1] "HARRIS_HYPOXIA"

## [1] "YU_MYC_TARGETS_DN"

## [1] "REACTOME_CLASS_B_2_SECRETIN_FAMILY_RECEPTORS"

## [1] "REACTOME_PHOSPHOLIPASE_C_MEDIATED_CASCADE"

## [1] "FURUKAWA_DUSP6_TARGETS_PCI35_DN"

## [1] "WINTER_HYPOXIA_DN"

## [1] "KEGG_CHRONIC_MYELOID_LEUKEMIA"

## [1] "PID_TCR_PATHWAY"

## [1] "VECCHI_GASTRIC_CANCER_EARLY_UP"

## [1] "RAMALHO_STEMNESS_UP"

## [1] "REACTOME_TRNA_AMINOACYLATION"

## [1] "PRAMOONJAGO_SOX4_TARGETS_UP"

## [1] "SHEDDEN_LUNG_CANCER_POOR_SURVIVAL_A6"

## [1] "SENESE_HDAC2_TARGETS_UP"

## [1] "KEGG_BLADDER_CANCER"

## [1] "SCHUHMACHER_MYC_TARGETS_UP"

## [1] "KEGG_AMINOACYL_TRNA_BIOSYNTHESIS"

## [1] "REACTOME_REGULATION_OF_INSULIN_SECRETION_BY_GLUCAGON_LIKE_PEPTIDE1"

## [1] "REACTOME_DAG_AND_IP3_SIGNALING"

## [1] "IVANOVSKA_MIR106B_TARGETS"

## [1] "BIOCARTA_RAS_PATHWAY"

## [1] "SHIPP_DLBCL_VS_FOLLICULAR_LYMPHOMA_UP"

## [1] "CROMER_METASTASIS_DN"

## [1] "AMIT_EGF_RESPONSE_480_MCF10A"

## [1] "MURAKAMI_UV_RESPONSE_6HR_UP"

## [1] "LIANG_HEMATOPOIESIS_STEM_CELL_NUMBER_SMALL_VS_HUGE_UP"

## [1] "LU_EZH2_TARGETS_DN"

## [1] "SESTO_RESPONSE_TO_UV_C2"

## [1] "MARTINEZ_RESPONSE_TO_TRABECTEDIN_DN"

## [1] "BIOCARTA_CXCR4_PATHWAY"

## [1] "BILD_MYC_ONCOGENIC_SIGNATURE"

## [1] "SMID_BREAST_CANCER_NORMAL_LIKE_UP"

## [1] "LEE_CALORIE_RESTRICTION_NEOCORTEX_DN"

## [1] "REACTOME_GLUCAGON_TYPE_LIGAND_RECEPTORS"

## [1] "LEONARD_HYPOXIA"

## [1] "COLLER_MYC_TARGETS_UP"

## [1] "BIOCARTA_MTOR_PATHWAY"

## [1] "KEGG_TASTE_TRANSDUCTION"

## [1] "SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_UP"

## [1] "KLEIN_PRIMARY_EFFUSION_LYMPHOMA_DN"

## [1] "GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN"

## [1] "SENESE_HDAC1_TARGETS_UP"

## [1] "SIMBULAN_UV_RESPONSE_IMMORTALIZED_DN"

## [1] "ELVIDGE_HIF1A_TARGETS_DN"

## [1] "NAKAMURA_CANCER_MICROENVIRONMENT_DN"

## [1] "PID_DELTA_NP63_PATHWAY"

## [1] "BERENJENO_TRANSFORMED_BY_RHOA_FOREVER_DN"

## [1] "REACTOME_IL1_SIGNALING"

## [1] "SWEET_KRAS_ONCOGENIC_SIGNATURE"

## [1] "ELVIDGE_HYPOXIA_UP"

## [1] "MANALO_HYPOXIA_UP"

## [1] "WILLERT_WNT_SIGNALING"

## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_4"

## [1] "LIAO_METASTASIS"

## [1] "BLUM_RESPONSE_TO_SALIRASIB_UP"

## [1] "AMIT_EGF_RESPONSE_480_HELA"

## [1] "BLALOCK_ALZHEIMERS_DISEASE_INCIPIENT_DN"

## [1] "GROSS_HYPOXIA_VIA_ELK3_DN"

## [1] "KEGG_VASOPRESSIN_REGULATED_WATER_REABSORPTION"

## [1] "BASAKI_YBX1_TARGETS_UP"

## [1] "REACTOME_CA_DEPENDENT_EVENTS"

## [1] "WANG_SMARCE1_TARGETS_DN"

## [1] "SCHLOSSER_MYC_TARGETS_AND_SERUM_RESPONSE_DN"

## [1] "WEI_MYCN_TARGETS_WITH_E_BOX"

## [1] "PID_A6B1_A6B4_INTEGRIN_PATHWAY"

## [1] "STARK_HYPPOCAMPUS_22Q11_DELETION_UP"

## [1] "GENTILE_RESPONSE_CLUSTER_D3"

## [1] "PID_MTOR_4PATHWAY"

## [1] "DANG_REGULATED_BY_MYC_UP"

## [1] "LI_AMPLIFIED_IN_LUNG_CANCER"

## [1] "LEI_MYB_TARGETS"

## [1] "REACTOME_METABOLISM_OF_NUCLEOTIDES"

## [1] "BIOCARTA_RACCYCD_PATHWAY"

## [1] "SMID_BREAST_CANCER_BASAL_UP"

## [1] "COULOUARN_TEMPORAL_TGFB1_SIGNATURE_UP"

## [1] "SMITH_TERT_TARGETS_UP"

## [1] "ALONSO_METASTASIS_EMT_UP"

## [1] "GRANDVAUX_IRF3_TARGETS_DN"

## [1] "KEGG_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM"

## [1] "REACTOME_PI_METABOLISM"

## [1] "ZHAN_MULTIPLE_MYELOMA_CD2_DN"

## [1] "CAFFAREL_RESPONSE_TO_THC_24HR_5_UP"

## [1] "NIKOLSKY_BREAST_CANCER_11Q12_Q14_AMPLICON"

## [1] "SMIRNOV_RESPONSE_TO_IR_2HR_DN"

## [1] "KEGG_ERBB_SIGNALING_PATHWAY"

## [1] "ZUCCHI_METASTASIS_DN"

## [1] "ZHOU_TNF_SIGNALING_30MIN"

## [1] "PID_TAP63_PATHWAY"

## [1] "KOKKINAKIS_METHIONINE_DEPRIVATION_96HR_DN"

## [1] "REACTOME_PYRIMIDINE_METABOLISM"

## [1] "NAKAMURA_TUMOR_ZONE_PERIPHERAL_VS_CENTRAL_DN"

## [1] "HOFMANN_CELL_LYMPHOMA_UP"

## [1] "BIOCARTA_FMLP_PATHWAY"

## [1] "PID_MYC_ACTIV_PATHWAY"

## [1] "CHARAFE_BREAST_CANCER_LUMINAL_VS_BASAL_DN"

## [1] "MOOTHA_GLUCONEOGENESIS"

## [1] "PID_EPHB_FWD_PATHWAY"

## [1] "KIM_WT1_TARGETS_8HR_UP"

## [1] "PID_UPA_UPAR_PATHWAY"

## [1] "SNIJDERS_AMPLIFIED_IN_HEAD_AND_NECK_TUMORS"

## [1] "FARMER_BREAST_CANCER_BASAL_VS_LULMINAL"

## [1] "BHAT_ESR1_TARGETS_VIA_AKT1_UP"

## [1] "SHEPARD_CRUSH_AND_BURN_MUTANT_UP"

## [1] "NUYTTEN_NIPP1_TARGETS_UP"

## [1] "DOANE_BREAST_CANCER_CLASSES_DN"

## [1] "SHAFFER_IRF4_TARGETS_IN_ACTIVATED_B_LYMPHOCYTE"

## [1] "CLIMENT_BREAST_CANCER_COPY_NUMBER_UP"

## [1] "THEILGAARD_NEUTROPHIL_AT_SKIN_WOUND_UP"

## [1] "SANA_RESPONSE_TO_IFNG_DN"

## [1] "KEGG_PYRIMIDINE_METABOLISM"

## [1] "KIM_WT1_TARGETS_UP"

## [1] "ZWANG_CLASS_3_TRANSIENTLY_INDUCED_BY_EGF"

## [1] "FRIDMAN_IMMORTALIZATION_DN"

## [1] "PEDERSEN_METASTASIS_BY_ERBB2_ISOFORM_7"

## [1] "ZHAN_MULTIPLE_MYELOMA_PR_UP"

## [1] "PHONG_TNF_RESPONSE_VIA_P38_PARTIAL"

## [1] "BIOCARTA_SPPA_PATHWAY"

## [1] "JIANG_HYPOXIA_NORMAL"

## [1] "WATANABE_RECTAL_CANCER_RADIOTHERAPY_RESPONSIVE_DN"

## [1] "DAZARD_UV_RESPONSE_CLUSTER_G2"

## [1] "RICKMAN_HEAD_AND_NECK_CANCER_D"

## [1] "CHEN_LVAD_SUPPORT_OF_FAILING_HEART_DN"

## [1] "PID_CD8_TCR_PATHWAY"

## [1] "GENTILE_UV_RESPONSE_CLUSTER_D5"

## [1] "BILD_HRAS_ONCOGENIC_SIGNATURE"

## [1] "LIM_MAMMARY_STEM_CELL_DN"

## [1] "DITTMER_PTHLH_TARGETS_UP"

## [1] "LIN_SILENCED_BY_TUMOR_MICROENVIRONMENT"

## [1] "WHITFIELD_CELL_CYCLE_G2_M"

## [1] "POMEROY_MEDULLOBLASTOMA_PROGNOSIS_UP"

## [1] "PID_NCADHERIN_PATHWAY"

## [1] "GENTILE_UV_RESPONSE_CLUSTER_D7"

## [1] "PID_HIF1_TFPATHWAY"

## [1] "NUNODA_RESPONSE_TO_DASATINIB_IMATINIB_UP"

## [1] "GROSS_HYPOXIA_VIA_ELK3_ONLY_UP"

## [1] "NEMETH_INFLAMMATORY_RESPONSE_LPS_UP"

## [1] "LINDGREN_BLADDER_CANCER_CLUSTER_3_DN"

## [1] "TONKS_TARGETS_OF_RUNX1_RUNX1T1_FUSION_MONOCYTE_UP"

## [1] "BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_UP"

## [1] "NUYTTEN_NIPP1_TARGETS_DN"

## [1] "SENESE_HDAC3_TARGETS_UP"

## [1] "MORI_SMALL_PRE_BII_LYMPHOCYTE_DN"

## [1] "PID_CERAMIDE_PATHWAY"

## [1] "DORSAM_HOXA9_TARGETS_UP"

## [1] "NATSUME_RESPONSE_TO_INTERFERON_BETA_DN"

## [1] "WANG_LMO4_TARGETS_DN"

## [1] "MOHANKUMAR_HOXA1_TARGETS_DN"

## [1] "ONDER_CDH1_TARGETS_1_DN"

## [1] "BENPORATH_MYC_TARGETS_WITH_EBOX"

## [1] "FERNANDEZ_BOUND_BY_MYC"

## [1] "GOTZMANN_EPITHELIAL_TO_MESENCHYMAL_TRANSITION_DN"

## [1] "KOKKINAKIS_METHIONINE_DEPRIVATION_48HR_UP"

## [1] "YAGI_AML_WITH_INV_16_TRANSLOCATION"

## [1] "FULCHER_INFLAMMATORY_RESPONSE_LECTIN_VS_LPS_UP"

## [1] "LINSLEY_MIR16_TARGETS"

## [1] "KEGG_ACUTE_MYELOID_LEUKEMIA"

## [1] "HOELZEL_NF1_TARGETS_UP"

## [1] "BHAT_ESR1_TARGETS_NOT_VIA_AKT1_UP"

## [1] "KEGG_PATHWAYS_IN_CANCER"

## [1] "BASSO_HAIRY_CELL_LEUKEMIA_UP"

## [1] "REACTOME_G_ALPHA_Z_SIGNALLING_EVENTS"

## [1] "GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_DN"

## [1] "BRUINS_UVC_RESPONSE_LATE"

## [1] "MARTINEZ_RB1_TARGETS_UP"

## [1] "DOUGLAS_BMI1_TARGETS_UP"

## [1] "ALFANO_MYC_TARGETS"

## [1] "RAMALHO_STEMNESS_DN"

## [1] "VANASSE_BCL2_TARGETS_DN"

## [1] "REACTOME_DARPP_32_EVENTS"

## [1] "CHANG_CORE_SERUM_RESPONSE_DN"

## [1] "ST_G_ALPHA_I_PATHWAY"

## [1] "REACTOME_RECYCLING_PATHWAY_OF_L1"

## [1] "WILENSKY_RESPONSE_TO_DARAPLADIB"

## [1] "BORCZUK_MALIGNANT_MESOTHELIOMA_DN"

## [1] "BIOCARTA_IL7_PATHWAY"

## [1] "REACTOME_MHC_CLASS_II_ANTIGEN_PRESENTATION"

## [1] "REACTOME_IMMUNOREGULATORY_INTERACTIONS_BETWEEN_A_LYMPHOID_AND_A_NON_LYMPHOID_CELL"

## [1] "RICKMAN_TUMOR_DIFFERENTIATED_WELL_VS_MODERATELY_UP"

## [1] "PID_RAC1_REG_PATHWAY"

## [1] "MIKKELSEN_IPS_WITH_HCP_H3K27ME3"

## [1] "ZHAN_MULTIPLE_MYELOMA_CD2_UP"

## [1] "ROVERSI_GLIOMA_COPY_NUMBER_UP"

## [1] "SCHLOSSER_SERUM_RESPONSE_UP"

## [1] "FERRANDO_T_ALL_WITH_MLL_ENL_FUSION_UP"

## [1] "MIKKELSEN_IPS_ICP_WITH_H3K27ME3"

## [1] "REACTOME_G_PROTEIN_ACTIVATION"

## [1] "REACTOME_ANTIGEN_ACTIVATES_B_CELL_RECEPTOR_LEADING_TO_GENERATION_OF_SECOND_MESSENGERS"

## [1] "CORRE_MULTIPLE_MYELOMA_DN"

## [1] "REACTOME_GLYCOSPHINGOLIPID_METABOLISM"

## [1] "BIOCARTA_CTLA4_PATHWAY"

## [1] "VECCHI_GASTRIC_CANCER_EARLY_DN"

## [1] "REACTOME_INTEGRATION_OF_ENERGY_METABOLISM"

## [1] "AKL_HTLV1_INFECTION_DN"

## [1] "KATSANOU_ELAVL1_TARGETS_UP"

## [1] "VALK_AML_WITH_FLT3_ITD"

## [1] "LEIN_MIDBRAIN_MARKERS"

## [1] "HUTTMANN_B_CLL_POOR_SURVIVAL_UP"

## [1] "KEGG_GNRH_SIGNALING_PATHWAY"

## [1] "LEE_LIVER_CANCER_SURVIVAL_UP"

## [1] "LEIN_LOCALIZED_TO_PROXIMAL_DENDRITES"

## [1] "KEGG_MELANOGENESIS"

## [1] "MA_MYELOID_DIFFERENTIATION_DN"

## [1] "REACTOME_REGULATION_OF_INSULIN_SECRETION"

## [1] "HANN_RESISTANCE_TO_BCL2_INHIBITOR_UP"

## [1] "GRADE_COLON_AND_RECTAL_CANCER_DN"

## [1] "ST_ADRENERGIC"

## [1] "CROMER_TUMORIGENESIS_DN"

## [1] "PID_IL3_PATHWAY"

## [1] "REACTOME_G_ALPHA_S_SIGNALLING_EVENTS"

## [1] "CHIARETTI_T_ALL_REFRACTORY_TO_THERAPY"

## [1] "MCCLUNG_COCAINE_REWARD_5D"

## [1] "REACTOME_DOWNSTREAM_SIGNALING_OF_ACTIVATED_FGFR"

## [1] "ZHANG_TARGETS_OF_EWSR1_FLI1_FUSION"

## [1] "MCCLUNG_DELTA_FOSB_TARGETS_8WK"

## [1] "NAKAYAMA_SOFT_TISSUE_TUMORS_PCA2_DN"

## [1] "KONDO_PROSTATE_CANCER_WITH_H3K27ME3"

## [1] "SANSOM_APC_TARGETS_DN"

## [1] "WNT_SIGNALING"

## [1] "KASLER_HDAC7_TARGETS_1_UP"

## [1] "REACTOME_COSTIMULATION_BY_THE_CD28_FAMILY"

## [1] "KEGG_GLYCEROPHOSPHOLIPID_METABOLISM"

## [1] "PEREZ_TP53_TARGETS"

## [1] "TAKEDA_TARGETS_OF_NUP98_HOXA9_FUSION_6HR_UP"

## [1] "PEREZ_TP63_TARGETS"